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Slight re-organization of C/C++ tools. Significant modifications to support observational data. Python and pipeline scripts added
This commit is contained in:
P.M. Sutter
parent
15496df4ff
commit
14abbc2018
42 changed files with 16252 additions and 557 deletions
550
c_tools/stacking/pruneVoids.cpp
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550
c_tools/stacking/pruneVoids.cpp
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// Reads in the void catalog and removes any void that could potentially
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// be affected by a mock particle. It does this by computing the longest
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// particle distance within each void and comparing it to the distance
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// of the nearest mock particle. If the void could potentially by rotated
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// to include this particle, we throw out the void.
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// This is placed here instead of using the edgeAvoidance option in
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// stackVoidsZero so that we can optionally filter the entire
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// catalog at once before the stacking phase. This is useful
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// for producing a "clean" void catalog for other purposes.
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#include "gsl/gsl_math.h"
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#include "string.h"
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#include "ctype.h"
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#include "stdlib.h"
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#include <math.h>
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#include <stdio.h>
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#include <netcdfcpp.h>
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#include "pruneVoids_conf.h"
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#define LIGHT_SPEED 299792.458
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#define MPC2Z 100./LIGHT_SPEED
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#define Z2MPC LIGHT_SPEED/100.
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typedef struct partStruct {
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float x, y, z, vol;
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} PART;
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typedef struct zoneStruct {
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int numPart;
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int *partIDs;
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} ZONE2PART;
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typedef struct voidZoneStruct {
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int numZones;
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int *zoneIDs;
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} VOID2ZONE;
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typedef struct voidStruct {
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float vol, coreDens, zoneVol, densCon, voidProb, radius;
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int voidID, numPart, numZones, coreParticle, zoneNumPart;
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float maxRadius, nearestMock, centralDen, redshift;
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float center[3], barycenter[3];
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int accepted;
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} VOID;
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int main(int argc, char **argv) {
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// initialize arguments
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pruneVoids_info args_info;
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pruneVoids_conf_params args_params;
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pruneVoids_conf_init(&args_info);
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pruneVoids_conf_params_init(&args_params);
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args_params.check_required = 0;
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if (pruneVoids_conf_ext (argc, argv, &args_info, &args_params))
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return 1;
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if (!args_info.configFile_given) {
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if (pruneVoids_conf_required (&args_info,
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PRUNEVOIDS_CONF_PACKAGE))
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return 1;
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} else {
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args_params.check_required = 1;
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args_params.initialize = 0;
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if (pruneVoids_conf_config_file (args_info.configFile_arg,
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&args_info,
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&args_params))
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return 1;
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}
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int i, p, p2, numPartTot, numZonesTot, dummy, iVoid, iZ;
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int numVoids, mockIndex, numKept;
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double tolerance;
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FILE *fp, *fpBarycenter, *fpDistances, *fpSkyPositions, *fpInfo;
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PART *part, *voidPart;
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ZONE2PART *zones2Parts;
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VOID2ZONE *void2Zones;
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VOID *voids;
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float *temp, junk, voidVol;
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int junkInt, voidID, numPart, numZones, zoneID, partID, maxNumPart;
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int coreParticle, zoneNumPart;
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float coreDens, zoneVol, densCon, voidProb, dist[3], dist2, minDist, maxDist;
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float centralRad, centralDen;
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double nearestEdge, redshift;
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char line[500], junkStr[10];
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int mask_index;
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double ranges[2][3], boxLen[3], mul;
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double volNorm, radius;
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int clock1, clock2;
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numVoids = args_info.numVoids_arg;
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mockIndex = args_info.mockIndex_arg;
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tolerance = args_info.tolerance_arg;
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clock1 = clock();
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printf("Pruning parameters: %f %f %f\n", args_info.zMin_arg,
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args_info.zMax_arg,
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args_info.rMin_arg);
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// load box size
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printf("\n Getting info...\n");
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NcFile f_info(args_info.extraInfo_arg);
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ranges[0][0] = f_info.get_att("range_x_min")->as_double(0);
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ranges[0][1] = f_info.get_att("range_x_max")->as_double(0);
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ranges[1][0] = f_info.get_att("range_y_min")->as_double(0);
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ranges[1][1] = f_info.get_att("range_y_max")->as_double(0);
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ranges[2][0] = f_info.get_att("range_z_min")->as_double(0);
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ranges[2][1] = f_info.get_att("range_z_max")->as_double(0);
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boxLen[0] = ranges[0][1] - ranges[0][0];
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boxLen[1] = ranges[1][1] - ranges[1][0];
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boxLen[2] = ranges[2][1] - ranges[2][0];
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// read in all particle positions
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printf("\n Loading particles...\n");
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fp = fopen(args_info.partFile_arg, "r");
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fread(&dummy, 1, 4, fp);
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fread(&numPartTot, 1, 4, fp);
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fread(&dummy, 1, 4, fp);
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part = (PART *) malloc(numPartTot * sizeof(PART));
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temp = (float *) malloc(numPartTot * sizeof(float));
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volNorm = numPartTot/(boxLen[0]*boxLen[1]*boxLen[2]);
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printf("VOL NORM = %f\n", volNorm);
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printf("CENTRAL DEN = %f\n", args_info.maxCentralDen_arg);
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fread(&dummy, 1, 4, fp);
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fread(temp, numPartTot, 4, fp);
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mul = ranges[0][1] - ranges[0][0];
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for (p = 0; p < numPartTot; p++)
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part[p].x = mul*temp[p];
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fread(&dummy, 1, 4, fp);
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fread(&dummy, 1, 4, fp);
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fread(temp, numPartTot, 4, fp);
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mul = ranges[1][1] - ranges[1][0];
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for (p = 0; p < numPartTot; p++)
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part[p].y = mul*temp[p];
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fread(&dummy, 1, 4, fp);
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fread(&dummy, 1, 4, fp);
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fread(temp, numPartTot, 4, fp);
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mul = ranges[2][1] - ranges[2][0];
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for (p = 0; p < numPartTot; p++)
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part[p].z = mul*temp[p];
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if (!args_info.isObservation_flag) {
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for (p = 0; p < numPartTot; p++) {
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part[p].x += ranges[0][0];
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part[p].y += ranges[1][0];
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part[p].z += ranges[2][0];
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}
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}
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fclose(fp);
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printf(" Read %d particles...\n", numPartTot);
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if (mockIndex == -1) mockIndex = numPartTot;
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// read in desired voids
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printf(" Loading voids...\n");
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fp = fopen(args_info.voidDesc_arg ,"r");
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fgets(line, sizeof(line), fp);
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sscanf(line, "%d %s %d %s", &junkInt, junkStr, &junkInt, junkStr);
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fgets(line, sizeof(line), fp);
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voids = (VOID *) malloc(numVoids * sizeof(VOID));
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i = 0;
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while (fgets(line, sizeof(line), fp) != NULL) {
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sscanf(line, "%d %d %d %f %f %d %d %f %d %f %f\n", &iVoid, &voidID,
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&coreParticle, &coreDens, &zoneVol, &zoneNumPart, &numZones,
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&voidVol, &numPart, &densCon, &voidProb);
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i++;
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voids[i-1].coreParticle = coreParticle;
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voids[i-1].zoneNumPart = zoneNumPart;
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voids[i-1].coreDens = coreDens;
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voids[i-1].zoneVol = zoneVol;
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voids[i-1].voidID = voidID;
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voids[i-1].vol = voidVol;
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voids[i-1].numPart = numPart;
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voids[i-1].numZones = numZones;
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voids[i-1].densCon = densCon;
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voids[i-1].voidProb = voidProb;
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voids[i-1].radius = pow(voidVol/volNorm*3./4./M_PI, 1./3.);
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voids[i-1].accepted = 1;
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}
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fclose(fp);
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// load up the zone membership for each void
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printf(" Loading void-zone membership info...\n");
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fp = fopen(args_info.void2Zone_arg, "r");
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fread(&numZonesTot, 1, 4, fp);
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void2Zones = (VOID2ZONE *) malloc(numZonesTot * sizeof(VOID2ZONE));
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for (iZ = 0; iZ < numZonesTot; iZ++) {
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fread(&numZones, 1, 4, fp);
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void2Zones[iZ].numZones = numZones;
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void2Zones[iZ].zoneIDs = (int *) malloc(numZones * sizeof(int));
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for (p = 0; p < numZones; p++) {
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fread(&void2Zones[iZ].zoneIDs[p], 1, 4, fp);
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}
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}
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fclose(fp);
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// now the particles-zone
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printf(" Loading particle-zone membership info...\n");
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fp = fopen(args_info.zone2Part_arg, "r");
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fread(&dummy, 1, 4, fp);
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fread(&numZonesTot, 1, 4, fp);
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zones2Parts = (ZONE2PART *) malloc(numZonesTot * sizeof(ZONE2PART));
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for (iZ = 0; iZ < numZonesTot; iZ++) {
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fread(&numPart, 1, 4, fp);
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zones2Parts[iZ].numPart = numPart;
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zones2Parts[iZ].partIDs = (int *) malloc(numPart * sizeof(int));
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for (p = 0; p < numPart; p++) {
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fread(&zones2Parts[iZ].partIDs[p], 1, 4, fp);
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}
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}
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// and finally volumes
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printf(" Loading particle volumes...\n");
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fp = fopen(args_info.partVol_arg, "r");
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fread(&mask_index, 1, 4, fp);
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if (mask_index != mockIndex) {
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printf("NON-MATCHING MOCK INDICES!? %d %d\n", mask_index, mockIndex);
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exit(-1);
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}
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for (p = 0; p < mask_index; p++) {
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fread(&temp[0], 1, 4, fp);
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part[p].vol = temp[0];
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}
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fclose(fp);
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free(temp);
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// check boundaries
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printf(" Computing void properties...\n");
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maxNumPart = 0;
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for (iVoid = 0; iVoid < numVoids; iVoid++) {
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if (voids[iVoid].numPart > maxNumPart) maxNumPart = voids[iVoid].numPart;
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}
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voidPart = (PART *) malloc(maxNumPart * sizeof(PART));
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for (iVoid = 0; iVoid < numVoids; iVoid++) {
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voidID = voids[iVoid].voidID;
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//printf(" DOING %d (of %d) %d %d\n", iVoid, numVoids, voidID,
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// voids[iVoid].numPart);
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voids[iVoid].center[0] = part[voids[iVoid].coreParticle].x;
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voids[iVoid].center[1] = part[voids[iVoid].coreParticle].y;
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voids[iVoid].center[2] = part[voids[iVoid].coreParticle].z;
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// first load up particles into a buffer
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i = 0;
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for (iZ = 0; iZ < void2Zones[voidID].numZones; iZ++) {
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zoneID = void2Zones[voidID].zoneIDs[iZ];
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for (p = 0; p < zones2Parts[zoneID].numPart; p++) {
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partID = zones2Parts[zoneID].partIDs[p];
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if (partID > mask_index ||
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(part[partID].vol < 1.e-27 && part[partID].vol > 0.)) {
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printf("BAD PART!? %d %d %e", partID, mask_index, part[partID].vol);
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exit(-1);
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}
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voidPart[i].x = part[partID].x;
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voidPart[i].y = part[partID].y;
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voidPart[i].z = part[partID].z;
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voidPart[i].vol = part[partID].vol;
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i++;
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}
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}
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// compute barycenters
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double weight = 0.;
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voids[iVoid].barycenter[0] = 0.;
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voids[iVoid].barycenter[1] = 0.;
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voids[iVoid].barycenter[2] = 0.;
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// TODO handle periodic boundaries?
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for (p = 0; p < voids[iVoid].numPart; p++) {
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dist[0] = voidPart[p].x - voids[iVoid].center[0];
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dist[1] = voidPart[p].y - voids[iVoid].center[1];
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dist[2] = voidPart[p].z - voids[iVoid].center[2];
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//if (!args_info.isObservation_flag) {
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// dist[0] = fmin(dist[0], abs(boxLen[0]-dist[0]));
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// dist[1] = fmin(dist[1], abs(boxLen[1]-dist[1]));
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// dist[2] = fmin(dist[2], abs(boxLen[2]-dist[2]));
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//}
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voids[iVoid].barycenter[0] += voidPart[p].vol*(dist[0]);
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voids[iVoid].barycenter[1] += voidPart[p].vol*(dist[1]);
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voids[iVoid].barycenter[2] += voidPart[p].vol*(dist[2]);
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weight += voidPart[p].vol;
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}
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voids[iVoid].barycenter[0] /= weight;
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voids[iVoid].barycenter[1] /= weight;
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voids[iVoid].barycenter[2] /= weight;
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voids[iVoid].barycenter[0] += voids[iVoid].center[0];
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voids[iVoid].barycenter[1] += voids[iVoid].center[1];
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voids[iVoid].barycenter[2] += voids[iVoid].center[2];
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// compute central density
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centralRad = voids[iVoid].radius/args_info.centralRadFrac_arg;
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centralRad *= centralRad;
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centralDen = 0.;
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for (p = 0; p < voids[iVoid].numPart; p++) {
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dist[0] = voidPart[p].x - voids[iVoid].barycenter[0];
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dist[1] = voidPart[p].y - voids[iVoid].barycenter[1];
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dist[2] = voidPart[p].z - voids[iVoid].barycenter[2];
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//if (!args_info.isObservation_flag) {
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// dist[0] = fmin(dist[0], abs(boxLen[0]-dist[0]));
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// dist[1] = fmin(dist[1], abs(boxLen[1]-dist[1]));
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// dist[2] = fmin(dist[2], abs(boxLen[2]-dist[2]));
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//}
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dist2 = pow(dist[0],2) + pow(dist[1],2) + pow(dist[2],2);
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if (dist2 < centralRad) centralDen += 1;
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}
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voids[iVoid].centralDen = centralDen / (4./3. * M_PI * pow(centralRad, 3./2.));
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// compute maximum extent
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if (args_info.isObservation_flag) {
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maxDist = 0.;
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for (p = 0; p < voids[iVoid].numPart; p++) {
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for (p2 = p; p2 < voids[iVoid].numPart; p2++) {
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dist[0] = voidPart[p].x - voidPart[p2].x;
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dist[1] = voidPart[p].y - voidPart[p2].y;
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dist[2] = voidPart[p].z - voidPart[p2].z;
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dist2 = pow(dist[0],2) + pow(dist[1],2) + pow(dist[2],2);
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if (dist2 > maxDist) maxDist = dist2;
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}
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}
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voids[iVoid].maxRadius = sqrt(maxDist)/2.;
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} else {
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maxDist = 0.;
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for (p = 0; p < voids[iVoid].numPart; p++) {
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dist[0] = voidPart[p].x - voids[iVoid].barycenter[0];
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dist[0] = voidPart[p].y - voids[iVoid].barycenter[1];
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dist[0] = voidPart[p].z - voids[iVoid].barycenter[2];
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dist2 = pow(dist[0],2) + pow(dist[1],2) + pow(dist[2],2);
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if (dist2 > maxDist) maxDist = dist2;
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}
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voids[iVoid].maxRadius = sqrt(maxDist);
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}
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if (args_info.isObservation_flag) {
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// compute distance from center to nearest mock
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minDist = 1.e99;
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for (p = mockIndex; p < numPartTot; p++) {
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dist[0] = voids[iVoid].barycenter[0] - part[p].x;
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dist[1] = voids[iVoid].barycenter[1] - part[p].y;
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dist[2] = voids[iVoid].barycenter[2] - part[p].z;
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dist2 = pow(dist[0],2) + pow(dist[1],2) + pow(dist[2],2);
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if (dist2 < minDist) minDist = dist2;
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}
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voids[iVoid].nearestMock = sqrt(minDist);
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} else {
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voids[iVoid].nearestMock = 1.e99;
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}
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if (args_info.isObservation_flag) {
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voids[iVoid].redshift =
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sqrt(pow(voids[iVoid].barycenter[0] - boxLen[0]/2.,2) +
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pow(voids[iVoid].barycenter[1] - boxLen[1]/2.,2) +
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pow(voids[iVoid].barycenter[2] - boxLen[2]/2.,2));
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voids[iVoid].redshift = voids[iVoid].redshift;
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redshift = voids[iVoid].redshift;
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nearestEdge = fmin(fabs(redshift-args_info.zMin_arg*LIGHT_SPEED),
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fabs(redshift-args_info.zMax_arg*LIGHT_SPEED));
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} else {
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voids[iVoid].redshift = voids[iVoid].barycenter[2]/LIGHT_SPEED*100.;
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nearestEdge = fmin(
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fabs(voids[iVoid].barycenter[0] - ranges[0][0]),
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fabs(voids[iVoid].barycenter[0] - ranges[0][1]));
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nearestEdge = fmin(nearestEdge,
|
||||
fabs(voids[iVoid].barycenter[1] - ranges[1][0]));
|
||||
nearestEdge = fmin(nearestEdge,
|
||||
fabs(voids[iVoid].barycenter[1] - ranges[1][1]));
|
||||
nearestEdge = fmin(nearestEdge,
|
||||
fabs(voids[iVoid].barycenter[2] - ranges[2][0]));
|
||||
nearestEdge = fmin(nearestEdge,
|
||||
fabs(voids[iVoid].barycenter[2] - ranges[2][1]));
|
||||
}
|
||||
|
||||
if (nearestEdge < voids[iVoid].nearestMock) {
|
||||
voids[iVoid].nearestMock = nearestEdge;
|
||||
}
|
||||
} // iVoid
|
||||
|
||||
printf(" Picking winners and losers...\n");
|
||||
numKept = numVoids;
|
||||
for (iVoid = 0; iVoid < numVoids; iVoid++) {
|
||||
if (strcmp(args_info.dataPortion_arg, "edge") == 0 &&
|
||||
tolerance*voids[iVoid].maxRadius < voids[iVoid].nearestMock) {
|
||||
numKept--;
|
||||
voids[iVoid].accepted = 0;
|
||||
}
|
||||
|
||||
if (strcmp(args_info.dataPortion_arg, "central") == 0 &&
|
||||
tolerance*voids[iVoid].maxRadius > voids[iVoid].nearestMock) {
|
||||
numKept--;
|
||||
voids[iVoid].accepted = 0;
|
||||
}
|
||||
|
||||
if (voids[iVoid].centralDen > args_info.maxCentralDen_arg) {
|
||||
numKept--;
|
||||
voids[iVoid].accepted = -1;
|
||||
}
|
||||
|
||||
if (voids[iVoid].radius < args_info.rMin_arg) {
|
||||
numKept--;
|
||||
voids[iVoid].accepted = 0;
|
||||
}
|
||||
}
|
||||
printf(" Number kept: %d (out of %d)\n", numKept, numVoids);
|
||||
|
||||
printf(" Output...\n");
|
||||
fp = fopen(args_info.output_arg, "w");
|
||||
fpBarycenter = fopen(args_info.outCenters_arg, "w");
|
||||
fpInfo = fopen(args_info.outInfo_arg, "w");
|
||||
fpDistances = fopen(args_info.outDistances_arg, "w");
|
||||
fpSkyPositions = fopen(args_info.outSkyPositions_arg, "w");
|
||||
fprintf(fp, "%d particles, %d voids.\n", mockIndex, numKept);
|
||||
fprintf(fp, "see column in master void file\n");
|
||||
fprintf(fpInfo, "# center x,y,z (Mpc/h), volume (normalized), radius (Mpc/h), redshift, volume (Mpc/h^3), void ID\n");
|
||||
fprintf(fpSkyPositions, "# RA, dec, redshift, radius (Mpc/h), void ID\n");
|
||||
for (iVoid = 0; iVoid < numVoids; iVoid++) {
|
||||
|
||||
if (voids[iVoid].accepted != 1) continue;
|
||||
|
||||
fprintf(fp, "%d %d %d %f %f %d %d %f %d %f %f\n",
|
||||
i,
|
||||
voids[iVoid].voidID,
|
||||
voids[iVoid].coreParticle,
|
||||
voids[iVoid].coreDens,
|
||||
voids[iVoid].zoneVol,
|
||||
voids[iVoid].zoneNumPart,
|
||||
voids[iVoid].numZones,
|
||||
voids[iVoid].vol,
|
||||
voids[iVoid].numPart,
|
||||
voids[iVoid].densCon,
|
||||
voids[iVoid].voidProb);
|
||||
|
||||
fprintf(fpBarycenter, "%d %e %e %e\n",
|
||||
voids[iVoid].voidID,
|
||||
voids[iVoid].barycenter[0],
|
||||
voids[iVoid].barycenter[1],
|
||||
voids[iVoid].barycenter[2]);
|
||||
|
||||
fprintf(fpDistances, "%d %e\n",
|
||||
voids[iVoid].voidID,
|
||||
voids[iVoid].nearestMock);
|
||||
|
||||
double outCenter[3];
|
||||
outCenter[0] = voids[iVoid].barycenter[0];
|
||||
outCenter[1] = voids[iVoid].barycenter[1];
|
||||
outCenter[2] = voids[iVoid].barycenter[2];
|
||||
|
||||
if (args_info.isObservation_flag) {
|
||||
outCenter[0] = (voids[iVoid].barycenter[0]-boxLen[0]/2.)*100.;
|
||||
outCenter[1] = (voids[iVoid].barycenter[1]-boxLen[1]/2.)*100.;
|
||||
outCenter[2] = (voids[iVoid].barycenter[2]-boxLen[2]/2.)*100.;
|
||||
}
|
||||
|
||||
fprintf(fpInfo, "%.2f %.2f %.2f %.2f %.2f %.5f %.2f %d\n",
|
||||
outCenter[0],
|
||||
outCenter[1],
|
||||
outCenter[2],
|
||||
voids[iVoid].vol,
|
||||
voids[iVoid].radius,
|
||||
voids[iVoid].redshift,
|
||||
4./3.*M_PI*pow(voids[iVoid].radius, 3),
|
||||
voids[iVoid].voidID
|
||||
);
|
||||
|
||||
fprintf(fpSkyPositions, "%.2f %.2f %.5f %.2f %d\n",
|
||||
atan((voids[iVoid].barycenter[1]-boxLen[1]/2.)/(voids[iVoid].barycenter[0]-boxLen[0]/2.)) * 180/M_PI + 180,
|
||||
asin((voids[iVoid].barycenter[2]-boxLen[2]/2.)/voids[iVoid].redshift) * 180/M_PI,
|
||||
voids[iVoid].redshift,
|
||||
voids[iVoid].radius,
|
||||
voids[iVoid].voidID);
|
||||
|
||||
}
|
||||
fclose(fp);
|
||||
fclose(fpInfo);
|
||||
fclose(fpBarycenter);
|
||||
fclose(fpDistances);
|
||||
|
||||
// print the centers catalog again but without central density cuts
|
||||
fpInfo = fopen(args_info.outNoCutInfo_arg, "w");
|
||||
fprintf(fpInfo, "# center x,y,z (km/s), volume (normalized), radius (Mpc/h), redshift, volume (Mpc/h^3), void ID\n");
|
||||
for (iVoid = 0; iVoid < numVoids; iVoid++) {
|
||||
|
||||
if (voids[iVoid].accepted == 0) continue;
|
||||
|
||||
double outCenter[3];
|
||||
outCenter[0] = voids[iVoid].barycenter[0];
|
||||
outCenter[1] = voids[iVoid].barycenter[1];
|
||||
outCenter[2] = voids[iVoid].barycenter[2];
|
||||
|
||||
if (args_info.isObservation_flag) {
|
||||
outCenter[0] = (voids[iVoid].barycenter[0]-boxLen[0]/2.)*100.;
|
||||
outCenter[1] = (voids[iVoid].barycenter[1]-boxLen[1]/2.)*100.;
|
||||
outCenter[2] = (voids[iVoid].barycenter[2]-boxLen[2]/2.)*100.;
|
||||
}
|
||||
|
||||
|
||||
fprintf(fpInfo, "%.2f %.2f %.2f %.2f %.2f %.5f %.2f %d\n",
|
||||
outCenter[0],
|
||||
outCenter[1],
|
||||
outCenter[2],
|
||||
voids[iVoid].vol,
|
||||
voids[iVoid].radius,
|
||||
voids[iVoid].redshift,
|
||||
4./3.*M_PI*pow(voids[iVoid].radius, 3),
|
||||
voids[iVoid].voidID);
|
||||
}
|
||||
fclose(fpInfo);
|
||||
|
||||
clock2 = clock();
|
||||
printf(" Time: %f sec (for %d voids)\n", (1.*clock2-clock1)/CLOCKS_PER_SEC, numVoids);
|
||||
clock1 = clock();
|
||||
|
||||
|
||||
printf("Done!\n");
|
||||
return 0;
|
||||
} // end main
|
||||
Loading…
Add table
Add a link
Reference in a new issue